The new Arena Nationala in Bucharest is magnificent. Its steep sides – the steepest permissible according to European law, apparently – are conducive to a good atmosphere, it's near enough the centre of town to make access relatively simple and the early teething problems with the pitch have been sorted out. After all the problems over funding and all the delays, Romania has ended up with a national stadium to be proud of. Sitting in the press box for last week's Europa League final – plug sockets and televisions aplenty, Ethernet cables at every seat – it was hard to believe this was the same city I first visited 11 years earlier.

I'm not going to pretend I understand the underlying economics, but to the naked eye, Bucharest is booming. There's construction work everywhere, old churches and monuments are emerging and, while there are still rotting concrete monstrosities dotted about, the glorious old apartments seem somehow more visible now. Before the second world war, Bucharest was known as the Paris of the East: a decade ago that seemed a terrible ironic jibe; now, you can see what people were talking about.

The comparison in the stadiums is telling as well. The first game I went to in Bucharest was a Dinamo-Steaua derby at the dilapidated Dinamo Stadium. It was a raw day and the fire brigade got so sick of flares being hurled on to the running track that they ended up turning their hoses on the fans clinging to the fence at the front of the stand. A few years later I remember sitting in the rickety metal box that served as a press box at the Lia Manoliu Stadium (the old national arena) for a Champions League qualifier between Dinamo and Manchester United, terrified of what might happen if the lightning that flickered overhead struck the roof.

The move to the Arena Nationala, where the only gripe was that the coffee ran out a couple of hours before kick-off, would suggest Romanian football is on the up, but you don't have to scratch very far below the surface to realise what a mess it still is. Midway through the first half of the Europa League final there was a minor pitch invasion, two fans charging across the pitch in protest at what has happened to Universitatea Craiova. The club, one of the oldest and most successful in Romanian history, was relegated to the second tier last season, which alone would have been bad enough.

What followed, though, was far worse. Supposedly because the club refused to end a civil legal action against its former coach, Victor Piturca, it was expelled from all official competition for a year and forced to release all of its players. You don't have to be a conspiracy theorist to wonder whether the outspoken attitude of the Universitatea owner, Adrian Mititelu, and his criticism of the league president, Dumitru Dragomir, and the federation (FRF) president Mircea Sandu may not have been the real cause. The Romanian court of appeal has ruled the ban illegal and Fifa has questioned its legitimacy, but the FRF remains unmoved.

At the same time as Universitatea were suspended, Politehnica Timisoara were relegated to Liga II. Poli, a team who havegone through far too many incarnations even to begin to keep track of, forever splintering and merging, reforming and relocating, finished second last season but were denied a licence under Articles 46 and 47 of the Rules of Licensing Clubs – essentially for being in debt and failing to present a balanced budget. Gloria Bistrita and Victoria Branesti were also found in breach of Article 47, as were Universitatea, who also managed to breach Articles 11 and 23.

Such a step would have been unprecedented, but it might just about have been possible to present it as part of a new approach of financial probity had it not been for the release of the transcripts of the FRF's tribunal in Gazeta Sporturilor in which Sandu appear to present the decision as a victory over Poli's owner Marian Iancu. "I [expletive] him, I'm stronger and I [expletive] him as a person," the transcript reads.

"Those leading Romanian football are a well-organised group," Iancu said. "When they plan something they carry it out, that's the conclusion we can draw. They were savouring a victory they had planned and for which they had given all their energy. The thirst of revenge determined Mircea Sandu to make that vulgar remark. Their words show how badly they wanted to destroy us. This proves that everything was premeditated."

Dragomir, meanwhile, although he had publicly supported Universitatea until a row with Mititelu, was shown to have been in favour of their dissolution. "These transcripts prove once more that the statutes and regulations they keep invoking do not matter for Sandu and Dragomir, their vested interests matter," Mititelu said. "It can be freely seen that U Craiova was abusively executed in order to have its players taken away, and that Timisoara was the victim of Mircea Sandu's revenge." The other clubs, he said, were "collateral victims".

Dubious as the behaviour of Sandu and Dragomir has been, though, it's hard to portray Mititelu as a victim. He regularly failed to pay players and managers on time and attacked other club owners, making accusations without proof. On Monday the General Assembly of the FRF decided to abolish Mititelu's team permanently, while granting the municipality of Craiova the right to enter a team in the second division next season.

That entity has the backing of Mititelu's local opponents and significant players from the Universitatea team that reached the Uefa Cup semi-final in 1983. They also plan to build a new 25,000-seater stadium and have the mayor's support. In other words, with Mititelu threatening legal challenges, the FRF has opened the way for yet another situation in which multiple variants of the same club compete for legitimacy, as happened with Poli Timisoara. There may well be an infinite number of Universitatea Craiovas playing in an infinite number of possible universes, but there's a problem when more than one turns up in the same reality.

And that's just one of the many scandals. The day before the Europa League final, the Cluj derby was abandoned following a mass brawl sparked when Cadú, the CFR captain, having converted a controversial penalty, celebrated with a gesture at Universitatea Cluj fans. The Universitatea goalkeeper, Mircea Bornescu, attacked him, players from both sides piled in, and then fans and security staff got involved.

Or take Unirea Urziceni. They were champions in 2009 under Dan Petrescu and, the following year, they beat Rangers 4-1 in the Champions League at Ibrox. It should have been a hugely positive story, but instead the next day the Romanian papers led with yet another polemic from the notorious Steaua owner Gigi Becali (see Said & Done, passim). Unirea's owner Dumitru Bucsaru effectively gave up at that, selling off his squad, replacing them with youth players on loan deals. Unirea, not surprisingly, were relegated in 2011, then didn't apply for a licence and were dissolved.

Scandal, conspiracy and base idiocy lurk everywhere. However promising things may look on the surface, however impressive the Arena Nationala, Romanian football is still essentially rotten.